It seems to be assumed that The Shadowed One, as the new possessor of Makuta Kojol's (Great Spirit Robot) viruses, now has access to a powerful weapon.

I'm hopeful somebody on here can explain why this is the case. The viruses were effective in taking down Mata Nui in his GSR form, but why are they dangerous in any other case? They would seem to be useless after the destruction of the Matoran Universe anyway. I don't see the connection, but then, I might be lacking either some critical piece of information or some semblance of intelligence.

Agreed; this subforum is here for discussions of various Bionicle things like this.

To actually answer your question, though, I'd say you're underestimating what these viruses can do. Mata Nui was taken down by a virus, yes, but that was just one virus. To my understanding, Makuta viruses can have any number of effects. Some are used to make Rahi, some are used to make the universe go to sleep. The ones that TSO is in possession of could have any number of uses, and if the leader of the Dark Hunters finds them valuable, they're probably quite dangerous.

If we assume that Mata Nui's AI doesn't differ much from that of the average MU inhabitant, then I suppose those viruses could potentially be used on any MU being to bring about the same effect? I.e. putting someone into a coma from which the being dies eventually?This would only insofar be more useful than assassination/poisoning or something in that regard in that except for Miserix and Alternate Teridax no one would have the means to do something against this virus while wounds can be treated and poisons countered with antidotes, I guess, though.

Or maybe The Shadowed One with access to viruses can now potentially figure out a way to create his own viruses?

EDIT:

As an afterthought - Maybe the amount of virus you need to affect someone is linked to the size of the target's systems or something such. So enough of a virus to knock out a giant robot could potentially also be used to knock out a sizeable portion of the MU's inhabitants instead? But I'm not sure if this really would be how viruses work.